Cora is balancing the analytic and human priorities here, especially with the OF rotation. Yes, playing JD in left is suboptimal. But then between the OF and DH there are 5 good players for 4 positions.
It's the same with the bullpen - putting guys in spots, see what he has. Obviously the first 50-60 games of the season are not spring training - but you want to learn about your team, and if there are some losses as a result, you kind of grin and bear it.